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--- documents:101029imagej_cui_lifconversion [2010/10/29 15:38] – kota
+++ documents:101029imagej_cui_lifconversion [2020/11/26 09:11] (current) – external edit 127.0.0.1
@@ Line 67: / Line 67: @@
 </sxh>
+===== ImpProps.java =====
+Accessing Image Physical Properties. Compiled class should be copied to the imageJ plugin folder. [[http://rsbweb.nih.gov/ij/plugins/imp-props.html|Original java code]] was modified to access image properties scales and dimensions.
+<sxh java>
+import ij.*;
+import ij.measure.Calibration;
+//import java.lang.Double;
+/**
+ * This simple class can be called from an ImageJ macro via the "call" mechanism to
+ * get and set the (string) properties of the active image (ImagePlus).
+ *
+ * call("ImpProps.setProperty", "<key>", "<value>");
+ *	set property <key> to <value>, returns <value> if successful,
+ *	"" otherwise (no active image)
+ *
+ * call("ImpProps.getProperty", "<key>");
+ *	returns value of property <key> if set, "" otherwise (not found or no active image)
+ *
+ * @see    ij.ImagePlus#setProperty
+ * @see    ij.ImagePlus#getProperty
+ *
+ * @author Joachim Wesner
+ * @author Leica Microsystems CMS GmbH
+ * @author joachim.wesner@leica-microsystems.com
+ * @version 2008-3-15
+ *
+ * @author Kota Miura
+ * cmci, embl
+ * added methods for setting image dimension sizes and pixel scales.
+ * this was done for setting these values in headless mode.
+ * @version 2010-10-28
+ * This class can be compiled with ImageJ's Plugins>Compile and Run command.
+ */
+public class ImpProps {
+	//kota
+	public static String getProperties() {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		Object prop = imp.getProperties();
+		if (prop != null && prop instanceof String)
+			return (String)prop;
+		else
+			return "";
+	}
+	public static String setProperty(String arg1, String arg2) {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		imp.setProperty(arg1, arg2);
+		imp.updateAndDraw();
+		return arg2;
+	}
+	public static String getProperty(String arg1) {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		Object prop = imp.getProperty(arg1);
+		if (prop != null && prop instanceof String)
+			return (String)prop;
+		else
+			return "";
+	}
+	//kota
+	public static int setCalibration(String unit, String spixelWidth, String spixelHeight, String spixelDepth){
+		double pixelWidth = java.lang.Double.parseDouble(spixelWidth);
+		double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
+		double pixelDepth = java.lang.Double.parseDouble(spixelDepth);
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return -1;
+		Calibration cal = imp.getCalibration();
+		cal.setUnit(unit);
+		cal.pixelWidth = pixelWidth;
+		cal.pixelHeight = pixelHeight;
+		cal.pixelDepth = pixelDepth;
+		imp.setCalibration(cal);
+		WindowManager.repaintImageWindows();
+		return 1;
+	}
+	//kota
+	public static int setCalibration(
+		String schannels, String sslices,
+			String sframes, String unit,
+				String spixelWidth, String spixelHeight,
+					String spixelDepth) {
+		int channels = java.lang.Integer.parseInt(schannels);
+		int slices   = java.lang.Integer.parseInt(sslices);
+		int frames   = java.lang.Integer.parseInt(sframes);
+		double pixelWidth  = java.lang.Double.parseDouble(spixelWidth);
+		double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
+		double pixelDepth  = java.lang.Double.parseDouble(spixelDepth);
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return -1;
+		int stackSize = imp.getImageStackSize();
+		if (channels*slices*frames==stackSize)
+ 			imp.setDimensions(channels, slices, frames);
+ 		else
+ 			IJ.error("Properties", "The product of channels ("+channels+"), slices ("+slices
+ 				+")\n and frames ("+frames+") must equal the stack size ("+stackSize+").");
+		Calibration cal = imp.getCalibration();
+		cal.setUnit(unit);
+		//cal.setTimeUnit(IJ.micronSymbol + "sec");
+		cal.pixelWidth = pixelWidth;
+		cal.pixelHeight = pixelHeight;
+		cal.pixelDepth = pixelDepth;
+		imp.setCalibration(cal);
+		WindowManager.repaintImageWindows();
+		return 1;
+	}
+}
+</sxh>
 ===== bfconvert help =====
-<quote>
+<blockquote>
 To convert a file between formats, run:
   bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand]
@@ Line 113: / Line 234: @@
 Each file would have a single image plane.
-</quote>
+</blockquote>
+===== LifOpenerCUI.ijm =====
+ImageJ macro for converting LIF stack series to multiple tiff stacks, together with setting physical parameters.
+<code>
+// converts LIF file to channel-separated tif stacks.
+// output files will be saved under the folder <LIF file name>_tifStack
+//bach command example
+/*
+/usr/struct/bin/java -cp /g/almf/software/ij/headless.jar:/g/almf/software/ij/ij-1.44h.jar -Djava.awt.headless=true ij.ImageJ -ijpath /g/almf/software/ij -batch /g/almf/software/ij/LifOpenerCUI.ijm /g/almf/miura/lif/laminedapi23012.lif
+*/
+// TODO: scale should be set as the propertiy of tiff file.
+// reading out of the scale from LIF is somehow not working, unlike it was done in 2009
+// metadata of .lif file would be saved as <filename.lif>.meta.txt
+//will be saved in the same directory.
+// TODO: program might return error if sequence is terminated abruptly.
+// for setting scale, plugin " ImpProp.class" is required.
+	srcfile = getArgument();		//cui
+//	srcfile = File.openDialog("Select a LIF File"); //gui
+	requires("1.43d");
+	run("Bio-Formats Macro Extensions");
+	path = srcfile;
+	name = File.getName(path);
+	dir = File.getParent(path);
+	DAPIch = 0;//getNumber("DAPI ch=?", 0);
+	FISHch = 1;//getNumber("FISH ch=?", 1);
+	metaname = name + ".meta.txt";
+	q = File.separator; //090912
+	metafullpath = dir+q+metaname;
+	metastr = File.openAsString(metafullpath);
+	workdir = File.getParent(srcfile);  //getDirectory("Choose a work space directory to save resulting files");
+	//create "tiffStack" folder under the gene folder (tiff stacks will have series No. and channel so no overlaps)
+	pathtifstack = workdir + q + name+ "_tifStack"; print(pathtifstack );
+	if (File.isDirectory(pathtifstack)==0) File.makeDirectory(pathtifstack);
+	Ext.setId(path);
+	Ext.getSeriesCount(seriesCount);
+	Ext.getCurrentFile(file);
+	Ext.close();
+	print("File:"+ file);
+	print("series total number" + seriesCount);
+	for (s=0; s<seriesCount; s++) {
+		seriesNum = s;
+		//Ext.setId(path); 			//out 090925 v4n
+		//Ext.setSeries(seriesNum);
+		//Ext.getSeriesName(seriesName);
+		//Ext.close(); //out 090925 v4n
+		if (s>0) refresh =0;
+		seriesName = OpenLIFSeriesOneChannel(path, name, seriesNum, DAPIch, 0, metastr);	//modified 090925
+		G_GID = getImageID();
+		savepath = pathtifstack + q+getTitle();
+		print(savepath);
+		saveAs("tiff", savepath);
+		close();
+		OpenLIFSeriesOneChannel(path, name, seriesNum, FISHch, 0, metastr);
+		G_RID = getImageID();
+		savepath = pathtifstack  + q+ getTitle();
+		print(savepath);
+		saveAs("tiff", savepath);
+		close();
+	}
+//working  maybe memory flashing problem, but not sure.
+/* 090907
+
+	- save tif file in a specified directory
+	- problem with DAPI appearance in the resulting window.  ---> seperate 2D analysis files in other macro?
+*/
+function OpenLIFSeriesOneChannel(id, name, seriesNum, ch, datasetOpened, metastr){
+	run("Bio-Formats Macro Extensions");
+	//if (datasetOpened ==0) Ext.setId(id);
+	Ext.setId(id);
+	Ext.setSeries(seriesNum);
+	Ext.getSeriesName(seriesName); print(seriesName);
+	Ext.getSizeZ(sizeZ);
+	Ext.getSizeC(sizeC);
+	Ext.getSizeT(sizeT);
+	Ext.getImageCount(imageCount);
+	print("ImageCount:"+imageCount);
+	calculatedCount = sizeZ*sizeC*sizeT;
+	print("...calculated"+sizeZ*sizeC*sizeT);
+	if (imageCount != calculatedCount) {
+		print();
+		exit();
+	}
+	sizeT = imageCount/sizeC/sizeZ;
+	print("C:"+sizeC+" Z:"+sizeZ+" T:"+sizeT);
+	newname = name+"_"+seriesNum+"_ch"+ch+".tif";
+	setBatchMode(true);
+	for (j=0; j<sizeT; j++){
+		for (i=0; i<sizeZ; i++){
+			currentZch0 = i*sizeC;
+			currentPlane = j*sizeZ*sizeC + i*sizeC;
+			Ext.openImage("t"+j+"_z"+i, currentPlane+ch);
+			if ((i==0) && (j==0))
+				stackID=getImageID();
+			else	{
+				run("Copy");
+				close;
+				selectImage(stackID);
+				run("Add Slice");
+				run("Paste");
+			}
+			//print(currentPlane);
+		}
+	}
+	rename(newname);
+	xscale = returnXscale(metastr);
+	yscale = returnYscale(metastr);
+	zscale = returnZscale(metastr);
+	tscale = 1;//returnTscale(metastr);
+	xscalemicron = parseFloat(xscale) * pow(10, 6);
+	yscalemicron = parseFloat(yscale) * pow(10, 6);
+	zscalemicron = parseFloat(zscale) * pow(10, 6);
+	op = "channels=1 slices="+sizeZ+" frames="+sizeT+" unit=micron pixel_width="+xscalemicron +" pixel_height="+yscalemicron +" voxel_depth="+zscalemicron +" frame=[0 sec] origin=0,0";
+	//since run("Properties...", op); cannot be used (AWT problem in headless)
+	//follwoing is a new plugin for setting image properties.
+	// ImpProp.class
+	SsizeC = ""+1;
+	SsizeZ = ""+sizeZ;
+	SsizeT = ""+sizeT;
+	Sxscalemicron = ""+xscalemicron;
+	Syscalemicron = ""+yscalemicron;
+	Szscalemicron = ""+zscalemicron;
+	call("ImpProps.setCalibration",
+		SsizeC, SsizeZ, SsizeT, "micron",
+		Sxscalemicron, Syscalemicron, Szscalemicron);
+	setBatchMode(false);
+	//if (datasetOpened ==0) Ext.close();
+	Ext.close();
+	return seriesName;
+}
+//zscale in micron
+function returnZscale(metastr){
+	metaA = split(metastr, "\n");
+	zscale = 1;
+	for (i=0; i<metaA.length; i++){
+		if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblStepSize")){
+			lineA = split(metaA[i], " ");
+			//for (j=0; j<lineA.length; j++)print(lineA[j]);
+			if (lineA.length>=3) {
+				zscale = parseFloat(lineA[2]);
+				print(zscale);
+			}
+		}
+	}
+	return zscale;
+}
+//Xscale in micron
+function returnXscale(metastr){
+	metaA = split(metastr, "\n");
+	xscale = 1;
+	for (i=0; i<metaA.length; i++){
+		if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblVoxelX")){
+			lineA = split(metaA[i], " ");
+			//for (j=0; j<lineA.length; j++)print(lineA[j]);
+			if (lineA.length>=3) {
+				xscale = parseFloat(lineA[2]);
+				print(xscale);
+			}
+		}
+	}
+	return xscale;
+}
+function returnYscale(metastr){
+	metaA = split(metastr, "\n");
+	yscale = 1;
+	for (i=0; i<metaA.length; i++){
+		if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblVoxelY")){
+			lineA = split(metaA[i], " ");
+			//for (j=0; j<lineA.length; j++)print(lineA[j]);
+			if (lineA.length>=3){
+				yscale = parseFloat(lineA[2]);
+				print(yscale);
+			}
+		}
+	}
+	return yscale;
+}
+function returnTscale(){
+	metaA = split(metastr, "\n");
+	for (i=0; i<metaA.length; i++){
+	if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblStepSize")){
+		lineA = split(metaA[i], " ");
+		//for (j=0; j<lineA.length; j++)print(lineA[j]);
+		if (lineA.length>=3) print(parseFloat(lineA[2]));
+	}
+	}
+}
+</code>